In fluorescence microscopy, a sample is labeled with a fluorescent dye, and then placed on the microscope using a sample holder. The sample holder positions the sample such that the front focal plane of the microscope's objective is coinciding with a region of the sample. The sample is then illuminated by one or more beams of light shining through the objective. In response, the fluorescent dye in the sample emits light that is usually at a wavelength that is substantially different from the wavelength of the illuminating light, and hence, the object stained by the dye can be distinguished from objects that did not absorb the dye. The microscope is configured such that light emitted by the sample is, by means of several lenses and mirrors, collected on a detector, typically a camera, which coincides with a plane that is conjugate to the objective focal plane mentioned above. This results in an image of the sample being formed on the detector.
There are a number of different fluorescence microscopy modes that are distinguished by the type of illumination. Different modes provide different advantages depending on the specific goals of the experiment in which the microscope is being used. Each type of illumination requires a different illumination pattern on the specimen. Typically, each illumination pattern corresponds to a different arrangement of optical elements for forming the desired illumination pattern on the specimen from a light source. The optical elements sometimes include a mask that selectively blocks some light from the source. Different patterns are characterized by different masks, and hence, in switching illumination patterns, the masks must be changed which necessitates keeping a collection of different masks, removing the existing mask and inserting a new mask.